molstar 3.2.0 → 3.4.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/LICENSE +20 -20
- package/README.md +197 -194
- package/build/viewer/embedded.html +43 -43
- package/build/viewer/index.html +106 -106
- package/build/viewer/molstar.css +1 -1
- package/build/viewer/molstar.js +1 -1
- package/lib/apps/docking-viewer/index.html +36 -36
- package/lib/apps/docking-viewer/index.js +0 -1
- package/lib/apps/docking-viewer/viewport.js +6 -6
- package/lib/apps/viewer/app.d.ts +7 -6
- package/lib/apps/viewer/app.js +2 -1
- package/lib/apps/viewer/embedded.html +43 -43
- package/lib/apps/viewer/index.html +106 -106
- package/lib/apps/viewer/index.js +0 -1
- package/lib/cli/chem-comp-dict/create-ions.js +0 -1
- package/lib/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
- package/lib/cli/chem-comp-dict/create-saccharides.js +67 -0
- package/lib/cli/chem-comp-dict/create-table.js +0 -1
- package/lib/cli/chem-comp-dict/util.js +0 -1
- package/lib/cli/cif2bcif/converter.js +0 -1
- package/lib/cli/cif2bcif/index.js +0 -1
- package/lib/cli/cifschema/index.js +0 -1
- package/lib/cli/cifschema/util/cif-dic.js +0 -1
- package/lib/cli/cifschema/util/generate.js +0 -1
- package/lib/cli/cifschema/util/helper.js +0 -1
- package/lib/cli/cifschema/util/schema.js +0 -1
- package/lib/cli/lipid-params/index.js +0 -1
- package/lib/cli/state-docs/index.js +0 -1
- package/lib/cli/state-docs/pd-to-md.js +0 -1
- package/lib/cli/structure-info/helpers.js +0 -1
- package/lib/cli/structure-info/model.js +0 -1
- package/lib/cli/structure-info/volume.js +0 -1
- package/lib/commonjs/apps/docking-viewer/index.js +12 -13
- package/lib/commonjs/apps/docking-viewer/viewport.js +38 -38
- package/lib/commonjs/apps/viewer/app.d.ts +7 -6
- package/lib/commonjs/apps/viewer/app.js +24 -23
- package/lib/commonjs/apps/viewer/index.js +1 -2
- package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -7
- package/lib/commonjs/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
- package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +69 -0
- package/lib/commonjs/cli/chem-comp-dict/create-table.js +8 -9
- package/lib/commonjs/cli/chem-comp-dict/util.js +17 -18
- package/lib/commonjs/cli/cif2bcif/converter.js +9 -10
- package/lib/commonjs/cli/cif2bcif/index.js +8 -9
- package/lib/commonjs/cli/cifschema/index.js +27 -28
- package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -2
- package/lib/commonjs/cli/cifschema/util/generate.js +0 -1
- package/lib/commonjs/cli/cifschema/util/helper.js +0 -1
- package/lib/commonjs/cli/cifschema/util/schema.js +0 -1
- package/lib/commonjs/cli/lipid-params/index.js +9 -10
- package/lib/commonjs/cli/state-docs/index.js +2 -3
- package/lib/commonjs/cli/state-docs/pd-to-md.js +0 -1
- package/lib/commonjs/cli/structure-info/helpers.js +11 -12
- package/lib/commonjs/cli/structure-info/model.js +15 -16
- package/lib/commonjs/cli/structure-info/volume.js +9 -10
- package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -4
- package/lib/commonjs/examples/alpha-orbitals/example-data.js +0 -1
- package/lib/commonjs/examples/alpha-orbitals/index.js +11 -12
- package/lib/commonjs/examples/basic-wrapper/coloring.js +0 -1
- package/lib/commonjs/examples/basic-wrapper/controls.js +2 -3
- package/lib/commonjs/examples/basic-wrapper/custom-theme.js +0 -1
- package/lib/commonjs/examples/basic-wrapper/index.js +22 -23
- package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -9
- package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -4
- package/lib/commonjs/examples/domain-annotation-server/schemas.js +0 -1
- package/lib/commonjs/examples/domain-annotation-server/server.js +6 -7
- package/lib/commonjs/examples/domain-annotation-server/test.js +3 -4
- package/lib/commonjs/examples/lighting/index.js +8 -9
- package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -3
- package/lib/commonjs/examples/proteopedia-wrapper/coloring.js +0 -1
- package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -5
- package/lib/commonjs/examples/proteopedia-wrapper/index.js +26 -27
- package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -3
- package/lib/commonjs/examples/task.js +15 -16
- package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -3
- package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -2
- package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -3
- package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -3
- package/lib/commonjs/extensions/alpha-orbitals/gpu/shader.frag.js +0 -1
- package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -3
- package/lib/commonjs/extensions/alpha-orbitals/spherical-functions.js +0 -1
- package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -14
- package/lib/commonjs/extensions/anvil/algorithm.js +13 -14
- package/lib/commonjs/extensions/anvil/behavior.js +14 -15
- package/lib/commonjs/extensions/anvil/prop.js +7 -8
- package/lib/commonjs/extensions/anvil/representation.js +5 -6
- package/lib/commonjs/extensions/cellpack/color/generate.js +0 -1
- package/lib/commonjs/extensions/cellpack/color/provided.js +0 -1
- package/lib/commonjs/extensions/cellpack/curve.js +0 -1
- package/lib/commonjs/extensions/cellpack/data.js +0 -1
- package/lib/commonjs/extensions/cellpack/index.js +1 -2
- package/lib/commonjs/extensions/cellpack/model.js +26 -25
- package/lib/commonjs/extensions/cellpack/preset.js +6 -7
- package/lib/commonjs/extensions/cellpack/property.js +3 -4
- package/lib/commonjs/extensions/cellpack/representation.js +2 -3
- package/lib/commonjs/extensions/cellpack/state.js +13 -14
- package/lib/commonjs/extensions/cellpack/util.js +14 -15
- package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -8
- package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +0 -1
- package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +5 -6
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -3
- package/lib/commonjs/extensions/dnatco/confal-pyramids/types.js +0 -1
- package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +1 -2
- package/lib/commonjs/extensions/dnatco/index.js +0 -1
- package/lib/commonjs/extensions/g3d/data.js +6 -7
- package/lib/commonjs/extensions/g3d/format.js +14 -15
- package/lib/commonjs/extensions/g3d/model.js +4 -5
- package/lib/commonjs/extensions/geo-export/controls.js +3 -4
- package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -10
- package/lib/commonjs/extensions/geo-export/index.js +1 -2
- package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -13
- package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -8
- package/lib/commonjs/extensions/geo-export/render-object-exporter.js +0 -1
- package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -8
- package/lib/commonjs/extensions/geo-export/ui.js +7 -8
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -10
- package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -10
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -5
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -5
- package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -6
- package/lib/commonjs/extensions/model-export/export.js +4 -5
- package/lib/commonjs/extensions/model-export/index.js +1 -2
- package/lib/commonjs/extensions/model-export/ui.js +5 -6
- package/lib/commonjs/extensions/mp4-export/controls.js +5 -6
- package/lib/commonjs/extensions/mp4-export/encoder.js +4 -5
- package/lib/commonjs/extensions/mp4-export/index.js +1 -2
- package/lib/commonjs/extensions/mp4-export/ui.js +5 -6
- package/lib/commonjs/extensions/pdbe/index.js +0 -1
- package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -3
- package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -3
- package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -2
- package/lib/commonjs/extensions/pdbe/structure-quality-report/color.js +0 -1
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -9
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -18
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -3
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -10
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -7
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -10
- package/lib/commonjs/extensions/rcsb/graphql/symmetry.gql.js +0 -1
- package/lib/commonjs/extensions/rcsb/graphql/types.d.ts +158 -1
- package/lib/commonjs/extensions/rcsb/graphql/types.js +0 -1
- package/lib/commonjs/extensions/rcsb/index.js +0 -1
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -18
- package/lib/commonjs/extensions/rcsb/validation-report/color/density-fit.js +0 -1
- package/lib/commonjs/extensions/rcsb/validation-report/color/geometry-quality.js +0 -1
- package/lib/commonjs/extensions/rcsb/validation-report/color/random-coil-index.js +0 -1
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -16
- package/lib/commonjs/extensions/rcsb/validation-report/representation.js +22 -6
- package/lib/commonjs/extensions/zenodo/index.d.ts +7 -0
- package/lib/commonjs/extensions/zenodo/index.js +35 -0
- package/lib/commonjs/extensions/zenodo/ui.d.ts +61 -0
- package/lib/commonjs/extensions/zenodo/ui.js +306 -0
- package/lib/commonjs/mol-canvas3d/camera/stereo.js +1 -2
- package/lib/commonjs/mol-canvas3d/camera/transition.js +0 -1
- package/lib/commonjs/mol-canvas3d/camera/util.js +1 -2
- package/lib/commonjs/mol-canvas3d/camera.js +2 -2
- package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +3 -1
- package/lib/commonjs/mol-canvas3d/canvas3d.js +46 -39
- package/lib/commonjs/mol-canvas3d/controls/object.js +0 -1
- package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -2
- package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -2
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -6
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -6
- package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -2
- package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -3
- package/lib/commonjs/mol-canvas3d/passes/draw.js +15 -13
- package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -4
- package/lib/commonjs/mol-canvas3d/passes/image.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/passes/image.js +1 -2
- package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -7
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.d.ts +1 -1
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +23 -10
- package/lib/commonjs/mol-canvas3d/passes/passes.js +0 -1
- package/lib/commonjs/mol-canvas3d/passes/pick.js +0 -1
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.d.ts +8 -1
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +60 -31
- package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -10
- package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -4
- package/lib/commonjs/mol-canvas3d/util.js +2 -3
- package/lib/commonjs/mol-data/db/column-helpers.js +0 -1
- package/lib/commonjs/mol-data/db/column.js +2 -3
- package/lib/commonjs/mol-data/db/database.js +0 -1
- package/lib/commonjs/mol-data/db/table.js +1 -2
- package/lib/commonjs/mol-data/db.js +1 -2
- package/lib/commonjs/mol-data/generic/hash-set.js +0 -1
- package/lib/commonjs/mol-data/generic/linked-list.js +0 -1
- package/lib/commonjs/mol-data/generic/unique-array.js +0 -1
- package/lib/commonjs/mol-data/generic.js +3 -4
- package/lib/commonjs/mol-data/index.js +4 -5
- package/lib/commonjs/mol-data/int/impl/interval.js +0 -1
- package/lib/commonjs/mol-data/int/impl/ordered-set.js +0 -1
- package/lib/commonjs/mol-data/int/impl/segmentation.js +0 -1
- package/lib/commonjs/mol-data/int/impl/sorted-array.js +0 -1
- package/lib/commonjs/mol-data/int/interval.js +1 -2
- package/lib/commonjs/mol-data/int/linked-index.js +0 -1
- package/lib/commonjs/mol-data/int/map.js +0 -1
- package/lib/commonjs/mol-data/int/ordered-set.js +1 -2
- package/lib/commonjs/mol-data/int/segmentation.js +1 -2
- package/lib/commonjs/mol-data/int/sorted-array.js +1 -2
- package/lib/commonjs/mol-data/int/sorted-ranges.js +0 -1
- package/lib/commonjs/mol-data/int/tuple.js +0 -1
- package/lib/commonjs/mol-data/int.js +0 -1
- package/lib/commonjs/mol-data/iterator.js +0 -1
- package/lib/commonjs/mol-data/util/array.js +0 -1
- package/lib/commonjs/mol-data/util/buckets.js +0 -1
- package/lib/commonjs/mol-data/util/chunked-array.js +0 -1
- package/lib/commonjs/mol-data/util/combination.js +0 -1
- package/lib/commonjs/mol-data/util/equivalence-classes.js +0 -1
- package/lib/commonjs/mol-data/util/grouping.js +0 -1
- package/lib/commonjs/mol-data/util/hash-functions.js +0 -1
- package/lib/commonjs/mol-data/util/interval-iterator.js +0 -1
- package/lib/commonjs/mol-data/util/sort.js +0 -1
- package/lib/commonjs/mol-data/util.js +7 -8
- package/lib/commonjs/mol-geo/geometry/base.js +0 -1
- package/lib/commonjs/mol-geo/geometry/clipping-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/color-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +2 -2
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +3 -4
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -4
- package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -2
- package/lib/commonjs/mol-geo/geometry/geometry.js +0 -1
- package/lib/commonjs/mol-geo/geometry/image/image.js +3 -4
- package/lib/commonjs/mol-geo/geometry/lines/lines-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +4 -5
- package/lib/commonjs/mol-geo/geometry/marker-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/axes.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/box.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/cylinder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/ellipsoid.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/ribbon.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/sheet.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/sphere.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/laplacian-smoothing.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +3 -4
- package/lib/commonjs/mol-geo/geometry/overpaint-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/picking.js +0 -1
- package/lib/commonjs/mol-geo/geometry/points/points-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/points/points.js +3 -4
- package/lib/commonjs/mol-geo/geometry/size-data.js +1 -2
- package/lib/commonjs/mol-geo/geometry/spheres/spheres-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +3 -4
- package/lib/commonjs/mol-geo/geometry/substance-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -2
- package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -3
- package/lib/commonjs/mol-geo/geometry/text/text.js +3 -4
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +4 -5
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +3 -4
- package/lib/commonjs/mol-geo/geometry/transform-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/transparency-data.js +0 -1
- package/lib/commonjs/mol-geo/primitive/box.js +0 -1
- package/lib/commonjs/mol-geo/primitive/cage.js +0 -1
- package/lib/commonjs/mol-geo/primitive/circle.js +1 -2
- package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -2
- package/lib/commonjs/mol-geo/primitive/dodecahedron.js +0 -1
- package/lib/commonjs/mol-geo/primitive/icosahedron.js +0 -1
- package/lib/commonjs/mol-geo/primitive/octahedron.js +0 -1
- package/lib/commonjs/mol-geo/primitive/plane.js +0 -1
- package/lib/commonjs/mol-geo/primitive/polygon.js +0 -1
- package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -2
- package/lib/commonjs/mol-geo/primitive/primitive.js +0 -1
- package/lib/commonjs/mol-geo/primitive/prism.js +1 -2
- package/lib/commonjs/mol-geo/primitive/pyramid.js +0 -1
- package/lib/commonjs/mol-geo/primitive/sphere.js +0 -1
- package/lib/commonjs/mol-geo/primitive/spiked-ball.js +0 -1
- package/lib/commonjs/mol-geo/primitive/star.js +1 -2
- package/lib/commonjs/mol-geo/primitive/tetrahedron.js +0 -1
- package/lib/commonjs/mol-geo/primitive/torus.js +1 -2
- package/lib/commonjs/mol-geo/primitive/wedge.js +0 -1
- package/lib/commonjs/mol-geo/util/location-iterator.js +0 -1
- package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -10
- package/lib/commonjs/mol-geo/util/marching-cubes/builder.js +0 -1
- package/lib/commonjs/mol-geo/util/marching-cubes/tables.js +0 -1
- package/lib/commonjs/mol-geo/util.js +0 -1
- package/lib/commonjs/mol-gl/commit-queue.js +0 -1
- package/lib/commonjs/mol-gl/compute/grid3d.js +5 -6
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -4
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -4
- package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -4
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -4
- package/lib/commonjs/mol-gl/compute/marching-cubes/tables.js +0 -1
- package/lib/commonjs/mol-gl/compute/util.js +3 -4
- package/lib/commonjs/mol-gl/object3d.js +0 -1
- package/lib/commonjs/mol-gl/render-object.js +0 -1
- package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -4
- package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -4
- package/lib/commonjs/mol-gl/renderable/image.js +3 -4
- package/lib/commonjs/mol-gl/renderable/lines.js +3 -4
- package/lib/commonjs/mol-gl/renderable/mesh.js +3 -4
- package/lib/commonjs/mol-gl/renderable/points.js +3 -4
- package/lib/commonjs/mol-gl/renderable/schema.js +1 -2
- package/lib/commonjs/mol-gl/renderable/spheres.js +3 -4
- package/lib/commonjs/mol-gl/renderable/text.js +3 -4
- package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -4
- package/lib/commonjs/mol-gl/renderable/util.js +1 -2
- package/lib/commonjs/mol-gl/renderable.js +0 -1
- package/lib/commonjs/mol-gl/renderer.js +3 -5
- package/lib/commonjs/mol-gl/scene.d.ts +2 -1
- package/lib/commonjs/mol-gl/scene.js +14 -3
- package/lib/commonjs/mol-gl/shader/chunks/apply-fog.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/apply-interior-color.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/apply-marker-color.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-clipping-varying.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/check-picking-alpha.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/clip-instance.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/clip-pixel.glsl.js +0 -1
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exports.StructureComplexElementTypes = exports.ShapeFromPly = exports.CustomStructureProperties = exports.CustomModelProperties = exports.StructureComponent = exports.StructureComplexElement = exports.StructureSelectionFromBundle = exports.StructureSelectionFromScript = exports.MultiStructureSelectionFromExpression = exports.StructureSelectionFromExpression = exports.TransformStructureConformation = exports.StructureFromModel = exports.StructureFromTrajectory = exports.ModelFromTrajectory = exports.TrajectoryFromCifCore = exports.TrajectoryFromCube = exports.TrajectoryFromMOL2 = exports.TrajectoryFromSDF = exports.TrajectoryFromMOL = exports.TrajectoryFromXYZ = exports.TrajectoryFromGRO = exports.TrajectoryFromPDB = exports.TrajectoryFromMmCif = exports.TrajectoryFromBlob = exports.TrajectoryFromModelAndCoordinates = exports.TopologyFromTop = exports.TopologyFromPrmtop = exports.TopologyFromPsf = exports.CoordinatesFromNctraj = exports.CoordinatesFromTrr = exports.CoordinatesFromXtc = exports.CoordinatesFromDcd = void 0;
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}
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});
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}); });
|
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}
|
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});
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|
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function getTrajectory(ctx, obj, coordinates) {
|
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|
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return
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if (!(obj.type === objects_1.PluginStateObject.Molecule.Topology.type)) return [3 /*break*/, 2];
|
|
@@ -155,9 +264,9 @@ var TrajectoryFromModelAndCoordinates = objects_1.PluginStateTransform.BuiltIn({
|
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|
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|
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|
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|
+
return mol_task_1.Task.create('Create trajectory from model/topology and coordinates', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
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|
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return tslib_1.__generator(this, function (_a) {
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|
coordinates = dependencies[params.coordinatesRef].data;
|
|
@@ -181,9 +290,9 @@ var TrajectoryFromBlob = objects_1.PluginStateTransform.BuiltIn({
|
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|
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return mol_task_1.Task.create('Parse Format Blob', function (ctx) { return
|
|
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|
+
return mol_task_1.Task.create('Parse Format Blob', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
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|
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|
|
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|
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return
|
|
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|
+
return tslib_1.__generator(this, function (_b) {
|
|
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|
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|
|
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|
case 0:
|
|
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|
models = [];
|
|
@@ -252,9 +361,9 @@ var TrajectoryFromMmCif = objects_1.PluginStateTransform.BuiltIn({
|
|
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|
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|
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|
|
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|
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|
|
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|
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return mol_task_1.Task.create('Parse mmCIF', function (ctx) { return
|
|
364
|
+
return mol_task_1.Task.create('Parse mmCIF', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
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|
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|
|
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|
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return
|
|
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|
+
return tslib_1.__generator(this, function (_a) {
|
|
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|
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|
|
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|
case 0:
|
|
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|
header = params.blockHeader || a.data.blocks[0].header;
|
|
@@ -286,9 +395,9 @@ var TrajectoryFromPDB = objects_1.PluginStateTransform.BuiltIn({
|
|
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|
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|
|
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|
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|
|
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|
var a = _a.a, params = _a.params;
|
|
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|
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return mol_task_1.Task.create('Parse PDB', function (ctx) { return
|
|
398
|
+
return mol_task_1.Task.create('Parse PDB', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
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|
var parsed, models, props;
|
|
291
|
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return
|
|
400
|
+
return tslib_1.__generator(this, function (_a) {
|
|
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|
switch (_a.label) {
|
|
293
402
|
case 0: return [4 /*yield*/, (0, parser_3.parsePDB)(a.data, a.label, params.isPdbqt).runInContext(ctx)];
|
|
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|
case 1:
|
|
@@ -315,9 +424,9 @@ var TrajectoryFromGRO = objects_1.PluginStateTransform.BuiltIn({
|
|
|
315
424
|
apply: function (_a) {
|
|
316
425
|
var _this = this;
|
|
317
426
|
var a = _a.a;
|
|
318
|
-
return mol_task_1.Task.create('Parse GRO', function (ctx) { return
|
|
427
|
+
return mol_task_1.Task.create('Parse GRO', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
319
428
|
var parsed, models, props;
|
|
320
|
-
return
|
|
429
|
+
return tslib_1.__generator(this, function (_a) {
|
|
321
430
|
switch (_a.label) {
|
|
322
431
|
case 0: return [4 /*yield*/, (0, parser_2.parseGRO)(a.data).runInContext(ctx)];
|
|
323
432
|
case 1:
|
|
@@ -344,9 +453,9 @@ var TrajectoryFromXYZ = objects_1.PluginStateTransform.BuiltIn({
|
|
|
344
453
|
apply: function (_a) {
|
|
345
454
|
var _this = this;
|
|
346
455
|
var a = _a.a;
|
|
347
|
-
return mol_task_1.Task.create('Parse XYZ', function (ctx) { return
|
|
456
|
+
return mol_task_1.Task.create('Parse XYZ', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
348
457
|
var parsed, models, props;
|
|
349
|
-
return
|
|
458
|
+
return tslib_1.__generator(this, function (_a) {
|
|
350
459
|
switch (_a.label) {
|
|
351
460
|
case 0: return [4 /*yield*/, (0, parser_7.parseXyz)(a.data).runInContext(ctx)];
|
|
352
461
|
case 1:
|
|
@@ -373,9 +482,9 @@ var TrajectoryFromMOL = objects_1.PluginStateTransform.BuiltIn({
|
|
|
373
482
|
apply: function (_a) {
|
|
374
483
|
var _this = this;
|
|
375
484
|
var a = _a.a;
|
|
376
|
-
return mol_task_1.Task.create('Parse MOL', function (ctx) { return
|
|
485
|
+
return mol_task_1.Task.create('Parse MOL', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
377
486
|
var parsed, models, props;
|
|
378
|
-
return
|
|
487
|
+
return tslib_1.__generator(this, function (_a) {
|
|
379
488
|
switch (_a.label) {
|
|
380
489
|
case 0: return [4 /*yield*/, (0, parser_4.parseMol)(a.data).runInContext(ctx)];
|
|
381
490
|
case 1:
|
|
@@ -402,9 +511,9 @@ var TrajectoryFromSDF = objects_1.PluginStateTransform.BuiltIn({
|
|
|
402
511
|
apply: function (_a) {
|
|
403
512
|
var _this = this;
|
|
404
513
|
var a = _a.a;
|
|
405
|
-
return mol_task_1.Task.create('Parse SDF', function (ctx) { return
|
|
514
|
+
return mol_task_1.Task.create('Parse SDF', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
406
515
|
var parsed, models, _i, _a, compound, traj_1, i, _b, _c, traj, props;
|
|
407
|
-
return
|
|
516
|
+
return tslib_1.__generator(this, function (_d) {
|
|
408
517
|
switch (_d.label) {
|
|
409
518
|
case 0: return [4 /*yield*/, (0, parser_8.parseSdf)(a.data).runInContext(ctx)];
|
|
410
519
|
case 1:
|
|
@@ -454,9 +563,9 @@ var TrajectoryFromMOL2 = objects_1.PluginStateTransform.BuiltIn({
|
|
|
454
563
|
apply: function (_a) {
|
|
455
564
|
var _this = this;
|
|
456
565
|
var a = _a.a;
|
|
457
|
-
return mol_task_1.Task.create('Parse MOL2', function (ctx) { return
|
|
566
|
+
return mol_task_1.Task.create('Parse MOL2', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
458
567
|
var parsed, models, props;
|
|
459
|
-
return
|
|
568
|
+
return tslib_1.__generator(this, function (_a) {
|
|
460
569
|
switch (_a.label) {
|
|
461
570
|
case 0: return [4 /*yield*/, (0, parser_5.parseMol2)(a.data, a.label).runInContext(ctx)];
|
|
462
571
|
case 1:
|
|
@@ -483,9 +592,9 @@ var TrajectoryFromCube = objects_1.PluginStateTransform.BuiltIn({
|
|
|
483
592
|
apply: function (_a) {
|
|
484
593
|
var _this = this;
|
|
485
594
|
var a = _a.a;
|
|
486
|
-
return mol_task_1.Task.create('Parse MOL', function (ctx) { return
|
|
595
|
+
return mol_task_1.Task.create('Parse MOL', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
487
596
|
var models, props;
|
|
488
|
-
return
|
|
597
|
+
return tslib_1.__generator(this, function (_a) {
|
|
489
598
|
switch (_a.label) {
|
|
490
599
|
case 0: return [4 /*yield*/, (0, cube_1.trajectoryFromCube)(a.data).runInContext(ctx)];
|
|
491
600
|
case 1:
|
|
@@ -518,9 +627,9 @@ var TrajectoryFromCifCore = objects_1.PluginStateTransform.BuiltIn({
|
|
|
518
627
|
apply: function (_a) {
|
|
519
628
|
var _this = this;
|
|
520
629
|
var a = _a.a, params = _a.params;
|
|
521
|
-
return mol_task_1.Task.create('Parse CIF Core', function (ctx) { return
|
|
630
|
+
return mol_task_1.Task.create('Parse CIF Core', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
522
631
|
var header, block, models, props;
|
|
523
|
-
return
|
|
632
|
+
return tslib_1.__generator(this, function (_a) {
|
|
524
633
|
switch (_a.label) {
|
|
525
634
|
case 0:
|
|
526
635
|
header = params.blockHeader || a.data.blocks[0].header;
|
|
@@ -557,9 +666,9 @@ var ModelFromTrajectory = objects_1.PluginStateTransform.BuiltIn({
|
|
|
557
666
|
apply: function (_a) {
|
|
558
667
|
var _this = this;
|
|
559
668
|
var a = _a.a, params = _a.params;
|
|
560
|
-
return mol_task_1.Task.create('Model from Trajectory', function (ctx) { return
|
|
669
|
+
return mol_task_1.Task.create('Model from Trajectory', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
561
670
|
var modelIndex, model, label, description;
|
|
562
|
-
return
|
|
671
|
+
return tslib_1.__generator(this, function (_a) {
|
|
563
672
|
switch (_a.label) {
|
|
564
673
|
case 0:
|
|
565
674
|
modelIndex = params.modelIndex % a.data.frameCount;
|
|
@@ -594,9 +703,9 @@ var StructureFromTrajectory = objects_1.PluginStateTransform.BuiltIn({
|
|
|
594
703
|
apply: function (_a) {
|
|
595
704
|
var _this = this;
|
|
596
705
|
var a = _a.a;
|
|
597
|
-
return mol_task_1.Task.create('Build Structure', function (ctx) { return
|
|
706
|
+
return mol_task_1.Task.create('Build Structure', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
598
707
|
var s, props;
|
|
599
|
-
return
|
|
708
|
+
return tslib_1.__generator(this, function (_a) {
|
|
600
709
|
switch (_a.label) {
|
|
601
710
|
case 0: return [4 /*yield*/, structure_1.Structure.ofTrajectory(a.data, ctx)];
|
|
602
711
|
case 1:
|
|
@@ -627,8 +736,8 @@ var StructureFromModel = objects_1.PluginStateTransform.BuiltIn({
|
|
|
627
736
|
apply: function (_a, plugin) {
|
|
628
737
|
var _this = this;
|
|
629
738
|
var a = _a.a, params = _a.params;
|
|
630
|
-
return mol_task_1.Task.create('Build Structure', function (ctx) { return
|
|
631
|
-
return
|
|
739
|
+
return mol_task_1.Task.create('Build Structure', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
740
|
+
return tslib_1.__generator(this, function (_a) {
|
|
632
741
|
return [2 /*return*/, root_structure_1.RootStructureDefinition.create(plugin, ctx, a.data, params && params.type)];
|
|
633
742
|
});
|
|
634
743
|
}); });
|
|
@@ -1031,7 +1140,7 @@ var StructureComplexElement = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1031
1140
|
query = structure_1.Queries.internal.spheres();
|
|
1032
1141
|
label = 'Coarse Spheres';
|
|
1033
1142
|
break;
|
|
1034
|
-
default:
|
|
1143
|
+
default: (0, type_helpers_1.assertUnreachable)(params.type);
|
|
1035
1144
|
}
|
|
1036
1145
|
var result = query(new structure_1.QueryContext(a.data));
|
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1037
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var s = structure_1.StructureSelection.unionStructure(result);
|
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@@ -1079,8 +1188,8 @@ var CustomModelProperties = objects_1.PluginStateTransform.BuiltIn({
|
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1079
1188
|
apply: function (_a, ctx) {
|
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1080
1189
|
var _this = this;
|
|
1081
1190
|
var a = _a.a, params = _a.params;
|
|
1082
|
-
return mol_task_1.Task.create('Custom Props', function (taskCtx) { return
|
|
1083
|
-
return
|
|
1191
|
+
return mol_task_1.Task.create('Custom Props', function (taskCtx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1192
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1084
1193
|
switch (_a.label) {
|
|
1085
1194
|
case 0: return [4 /*yield*/, attachModelProps(a.data, ctx, taskCtx, params)];
|
|
1086
1195
|
case 1:
|
|
@@ -1093,9 +1202,9 @@ var CustomModelProperties = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1093
1202
|
update: function (_a, ctx) {
|
|
1094
1203
|
var _this = this;
|
|
1095
1204
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1096
|
-
return mol_task_1.Task.create('Custom Props', function (taskCtx) { return
|
|
1205
|
+
return mol_task_1.Task.create('Custom Props', function (taskCtx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1097
1206
|
var _i, _a, name_1, property;
|
|
1098
|
-
return
|
|
1207
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1099
1208
|
switch (_b.label) {
|
|
1100
1209
|
case 0:
|
|
1101
1210
|
b.data = a.data;
|
|
@@ -1123,9 +1232,9 @@ var CustomModelProperties = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1123
1232
|
});
|
|
1124
1233
|
exports.CustomModelProperties = CustomModelProperties;
|
|
1125
1234
|
function attachModelProps(model, ctx, taskCtx, params) {
|
|
1126
|
-
return
|
|
1235
|
+
return tslib_1.__awaiter(this, void 0, void 0, function () {
|
|
1127
1236
|
var propertyCtx, autoAttach, properties, _i, _a, name_2, property, props, e_1;
|
|
1128
|
-
return
|
|
1237
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1129
1238
|
switch (_b.label) {
|
|
1130
1239
|
case 0:
|
|
1131
1240
|
propertyCtx = { runtime: taskCtx, assetManager: ctx.managers.asset };
|
|
@@ -1174,8 +1283,8 @@ var CustomStructureProperties = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1174
1283
|
apply: function (_a, ctx) {
|
|
1175
1284
|
var _this = this;
|
|
1176
1285
|
var a = _a.a, params = _a.params;
|
|
1177
|
-
return mol_task_1.Task.create('Custom Props', function (taskCtx) { return
|
|
1178
|
-
return
|
|
1286
|
+
return mol_task_1.Task.create('Custom Props', function (taskCtx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1287
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1179
1288
|
switch (_a.label) {
|
|
1180
1289
|
case 0: return [4 /*yield*/, attachStructureProps(a.data.root, ctx, taskCtx, params)];
|
|
1181
1290
|
case 1:
|
|
@@ -1190,9 +1299,9 @@ var CustomStructureProperties = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1190
1299
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1191
1300
|
if (a.data !== b.data)
|
|
1192
1301
|
return mol_state_1.StateTransformer.UpdateResult.Recreate;
|
|
1193
|
-
return mol_task_1.Task.create('Custom Props', function (taskCtx) { return
|
|
1302
|
+
return mol_task_1.Task.create('Custom Props', function (taskCtx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1194
1303
|
var _i, _a, name_3, property;
|
|
1195
|
-
return
|
|
1304
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1196
1305
|
switch (_b.label) {
|
|
1197
1306
|
case 0:
|
|
1198
1307
|
b.data = a.data;
|
|
@@ -1220,9 +1329,9 @@ var CustomStructureProperties = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1220
1329
|
});
|
|
1221
1330
|
exports.CustomStructureProperties = CustomStructureProperties;
|
|
1222
1331
|
function attachStructureProps(structure, ctx, taskCtx, params) {
|
|
1223
|
-
return
|
|
1332
|
+
return tslib_1.__awaiter(this, void 0, void 0, function () {
|
|
1224
1333
|
var propertyCtx, autoAttach, properties, _i, _a, name_4, property, props, e_2;
|
|
1225
|
-
return
|
|
1334
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1226
1335
|
switch (_b.label) {
|
|
1227
1336
|
case 0:
|
|
1228
1337
|
propertyCtx = { runtime: taskCtx, assetManager: ctx.managers.asset };
|
|
@@ -1270,9 +1379,9 @@ var ShapeFromPly = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1270
1379
|
apply: function (_a) {
|
|
1271
1380
|
var _this = this;
|
|
1272
1381
|
var a = _a.a, params = _a.params;
|
|
1273
|
-
return mol_task_1.Task.create('Create shape from PLY', function (ctx) { return
|
|
1382
|
+
return mol_task_1.Task.create('Create shape from PLY', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1274
1383
|
var shape, props;
|
|
1275
|
-
return
|
|
1384
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1276
1385
|
switch (_a.label) {
|
|
1277
1386
|
case 0: return [4 /*yield*/, (0, ply_1.shapeFromPly)(a.data, params).runInContext(ctx)];
|
|
1278
1387
|
case 1:
|
|
@@ -1285,4 +1394,3 @@ var ShapeFromPly = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1285
1394
|
}
|
|
1286
1395
|
});
|
|
1287
1396
|
exports.ShapeFromPly = ShapeFromPly;
|
|
1288
|
-
//# sourceMappingURL=model.js.map
|